Warning messages are not handled correctly

[nlewo]

With the latest release, when loading a library that return warning messages, the kernel fails.

In []: require(RDatalake)
Loading required package: RDatalake
Error in if (w$call != "eval(parse(text = code), envir = .GlobalEnv)") message(w,  : 
  argument is of length zero
Calls: <Anonymous> ... doTryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>

This library can be loaded in the R interpreter:

> require(RDatalake)
Loading required package: RDatalake
Warning messages:
1: replacing previous import ‘dplyr::sql’ by ‘dbplyr::sql’ when loading ‘RDatalake’ 
2: replacing previous import ‘dplyr::ident’ by ‘dbplyr::ident’ when loading ‘RDatalake’ 
> 

It is possible to load this library in the kernel if warning messages are ignored:

in []: suppressWarnings(require(RDatalake))
Loading required package: RDatalake

With the release 1.2.3.0, the library can be loaded. So, it seems this regression has been introduced by the commit 00c4d73.

I can try patches if needed.
Thanks.

cc @spennihana

[spennihana]

Hiya,

A patch here would be most welcome! I would want to make sure we don't regress #24, so let me push a test to inst/runits for that.

By the way, can you create a reproducible example? It appears that RDataLake may be your custom package.

[spennihana]

@nlewo ok test added: https://github.com/JuniperKernel/JuniperKernel/blob/master/inst/runits/runit.testWarnings.R

[spennihana]

@nlewo is this still a problem for you? I would like to resolve this issue.

[idontgetoutmuch]

I am experiencing this problem when using the package rstan.

[idontgetoutmuch]

@nlewo I tried copying what you did but get

installing via 'install.libs.R' to /nix/store/yggpnwrsawhx5qajafwjydzj4hih3cjv-r-JupiterKernel/library/00LOCK-JuniperKernel/00new/JuniperKernel
sh: which: command not found
Error in system("which install_name_tool", intern = TRUE) :
  error in running command
* removing '/nix/store/yggpnwrsawhx5qajafwjydzj4hih3cjv-r-JupiterKernel/library/JuniperKernel'
builder for '/nix/store/da72h8j1afm8wi1430fvl3hm02x0sxyr-r-JupiterKernel.drv' failed with exit code 1
cannot build derivation '/nix/store/lc29rgz92bhcrsysaz1fb7wvkhqzf8bp-R-3.6.1-wrapper.drv': 1 dependencies couldn't be built
error: build of '/nix/store/6c7vajxk7irrk7jlijd8znaazi8kga2w-jupyter-R-kernel.drv', '/nix/store/lc29rgz92bhcrsysaz1fb7wvkhqzf8bp-R-3.6.1-wrapper.drv' failed

let
pkgs = import <nixpkgs> {};
in

let

fontsConf = pkgs.makeFontsConf { fontDirectories = [ ];  };

my-R-packages = with pkgs.rPackages; [ rstan zoo ggplot2 dplyr coda ];

buildRPackage =
    pkgs.callPackage "${pkgs.path}/pkgs/development/r-modules/generic-builder.nix"
    { Cocoa = null; Foundation = null; };

JuniperKernel_1_2_3_0 = buildRPackage {
    name = "JupiterKernel";
    src = pkgs.fetchurl {
      url = https://cran.r-project.org/src/contrib/Archive/JuniperKernel/JuniperKernel_1.2.3.0.tar.gz;
      sha256 = "17r4ssjjayvnp9fp9jalklp3p8dadyx5hvi9z3bh3sw4b7kx4lyd";
    };
    preConfigure = ''
        patchShebangs configure
      '';
    requireX = false;
    propagatedBuildInputs = with pkgs.rPackages; [ data_table gdtools jsonlite pbdZMQ Rcpp repr ];
    nativeBuildInputs = with pkgs.rPackages; [ data_table gdtools jsonlite pbdZMQ Rcpp repr ];
  };

R-with-my-packages = pkgs.rWrapper.override{ packages = with pkgs.rPackages; my-R-packages ++ [ JuniperKernel_1_2_3_0 ]; };

jupyter-R-kernel = pkgs.stdenv.mkDerivation {
  name = "jupyter-R-kernel";
  buildInputs = [ pkgs.python36Packages.notebook R-with-my-packages pkgs.which ];
  unpackPhase = ":";
  installPhase = ''
    export HOME=$TMP
    echo $JUPYTER_PATH
    ${R-with-my-packages}/bin/R --slave -e "JuniperKernel::listKernels()"
    ${R-with-my-packages}/bin/R --slave -e "JuniperKernel::installJuniper(prefix='$out')"
  '';
};
in
pkgs.mkShell rec {
  name = "jupyter-with-R-kernel";
  buildInputs = [ pkgs.libintl jupyter-R-kernel pkgs.python36Packages.jupyter pkgs.which ];
  shellHook = ''
    export FONTCONFIG_FILE=${fontsConf}
    # Fontconfig error: Cannot load default config file
    export JUPYTER_PATH=${jupyter-R-kernel}/share/jupyter
    # see https://github.com/NixOS/nixpkgs/issues/38733
    ${R-with-my-packages}/bin/R --slave -e "system2('jupyter', 'notebook')"
  '';
}

[idontgetoutmuch]

@nlewo I needed buildInputs = [ pkgs.which pkgs.R pkgs.libintl ]; and now all is well using the old version of JuniperKernel. Sorry for the noise.